scholarly journals Distinct Expression Patterns of ICK/MAK/MOK Protein Kinases in the Intestine Implicate Functional Diversity

PLoS ONE ◽  
2013 ◽  
Vol 8 (11) ◽  
pp. e79359 ◽  
Author(s):  
Tufeng Chen ◽  
Di Wu ◽  
Christopher A. Moskaluk ◽  
Zheng Fu
Keyword(s):  
Protein Kinases ◽  
Functional Diversity ◽  
Expression Patterns

scholarly journals Expression Patterns of Protein Kinases Correlate with Gene Architecture and Evolutionary Rates

PLoS ONE ◽  
2008 ◽  
Vol 3 (10) ◽  
pp. e3599 ◽  
Author(s):  
Aleksey Y. Ogurtsov ◽  
Leonardo Mariño-Ramírez ◽  
Gibbes R. Johnson ◽  
David Landsman ◽  
Svetlana A. Shabalina ◽  
...  
Keyword(s):  
Protein Kinases ◽  
Expression Patterns ◽  
Evolutionary Rates ◽  
Gene Architecture

scholarly journals The wild strawberry kinome: identification, classification and transcript profiling of protein kinases during development and in response to gray mold infection

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Hui Liu ◽  
Wei Qu ◽  
Kaikai Zhu ◽  
Zong-Ming Cheng
Keyword(s):  
Protein Kinases ◽  
Evolutionary Dynamics ◽  
Expression Patterns ◽  
Gene Families ◽  
Gray Mold ◽  
Fragaria Vesca ◽  
Woodland Strawberry ◽  
Go Enrichment ◽  
Potential Link ◽  
Wild Strawberry

Abstract Background Protein kinases (PKs) play an important role in signaling cascades and are one of the largest and most conserved protein super families in plants. Despite their importance, the woodland strawberry (Fragaria vesca) kinome and expression patterns of PK genes remain to be characterized. Results Here, we report on the identification and classification of 954 Fragaria vesca PK genes, which were classified into nine groups and 124 gene families. These genes were distributed unevenly among the seven chromosomes, and the number of introns per gene varied from 0 to 47. Almost half of the putative PKs were predicted to localize to the nucleus and 24.6% were predicted to localize to the cell membrane. The expansion of the woodland strawberry PK gene family occurred via different duplication mechanisms and tandem duplicates occurred relatively late as compared to other duplication types. Moreover, we found that tandem and transposed duplicated PK gene pairs had undergone stronger diversifying selection and evolved relatively faster than WGD genes. The GO enrichment and transcriptome analysis implicates the involvement of strawberry PK genes in multiple biological processes and molecular functions in differential tissues, especially in pollens. Finally, 109 PKs, mostly the receptor-like kinases (RLKs), were found transcriptionally responsive to Botrytis cinerea infection. Conclusions The findings of this research expand the understanding of the evolutionary dynamics of PK genes in plant species and provide a potential link between cell signaling pathways and pathogen attack.

scholarly journals Comparative Analysis of HSF Genes From Secale cereale and its Triticeae Relatives Reveal Ancient and Recent Gene Expansions

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiao-Tong Li ◽  
Xing-Yu Feng ◽  
Zhen Zeng ◽  
Yang Liu ◽  
Zhu-Qing Shao
Keyword(s):  
Functional Diversity ◽  
Secale Cereale ◽  
Developmental Stages ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Chromosome Analysis ◽  
Regulation System ◽  
Chromosome 4 ◽  
Evolutionary Features ◽  
Adverse Environmental Conditions

Plants have evolved sophisticated systems to cope with the environmental stresses, with the heat shock factor (HSF) family proteins composing an integral part of the transcriptional regulation system. Understanding the evolutionary history and functional diversity of HSFs will facilitate improving tolerance of crops to adverse environmental conditions. In this study, genome-wide analysis of Secale cereale identified 31 HSF genes. The total number of HSF genes in S. cereale is larger than that in barley and the three subgenomes of wheat, suggesting it is a valuable resource for mining functional HSFs. Chromosome analysis revealed an uneven distribution of HSF genes among the 7 S. cereale chromosomes, with no HSF gene was detected on chromosome 4. Further interspecies synteny analysis revealed that chromosome reorganization during species-speciation may lead to the escape of HSF genes from the S. cereale chromosome 4. Phylogenetic analysis revealed that S. cereale experienced more HSF gene duplications than barley and the three wheat subgenomes. Expression analysis demonstrated that S. cereale HSF genes showed diverse expression patterns across plant developmental stages and upon drought and freezing treatment, suggesting functional diversity of the gene family. Notably, we detected distinct expression patterns for a recently duplicated HSF gene pair, indicating functional divergence may have occurred between the two genes. The study presents the genome organization, evolutionary features and expression patterns of the S. cereale HSF genes. These results provide new insights into the evolution of HSF genes in Triticeae and may serve as a resource for Triticeae molecular breeding.

scholarly journals Genomic Characterization and Expression Analysis of the SnRK family genes in Dendrobium officinale Kimura et Migo (Orchidaceae)

Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 479
Author(s):  
Yue Wang ◽  
Aizhong Liu
Keyword(s):  
Protein Kinases ◽  
Expression Patterns ◽  
Dendrobium Officinale ◽  
Limited Information ◽  
Related Protein ◽  
Quantitative Real Time Pcr ◽  
Sequencing Data ◽  
Promoter Regions ◽  
Plant Life ◽  
Genomic Characterization

Sucrose non-fermenting1-related protein kinases (SnRKs) are a type of Ser/Thr protein kinases, and they play an important role in plant life, especially in metabolism and responses to environmental stresses. However, there is limited information on SnRK genes in Dendrobium officinale. In the present research, a total of 36 DoSnRK genes were identified based on genomic data. These DoSnRKs could be grouped into three subfamilies, including 1 member of DoSnRK1, 7 of DoSnRK2, and 28 of DoSnRK3. The gene structure analysis of DoSnRK genes showed that 17 members had no introns, while 16 members contained six or more introns. The conserved domains and motifs were found in the same subfamily. The various cis-elements present in the promoter regions showed that DoSnRK genes could respond to stresses and hormones. Furthermore, the expression patterns of DoSnRK genes in eight tissues were investigated according to RNA sequencing data, indicating that multiple DoSnRK genes were ubiquitously expressed in these tissues. The transcript levels of DoSnRK genes after drought, MeJA, and ABA treatments were analyzed by quantitative real-time PCR and showed that most DoSnRK genes could respond to these stresses. Therefore, genomic characterization and expression analyses provide valuable information on DoSnRK genes for further understanding the functions of SnRKs in plants.

Diversity and Expression Patterns of MADS-Box Genes in Gnetum luofuense—Implications for Functional Diversity and Evolution

2019 ◽  
Vol 13 (1) ◽  
pp. 36-49 ◽  
Author(s):  
Chen Hou ◽  
Lingfei Li ◽  
Zhiming Liu ◽  
Yingjuan Su ◽  
Tao Wan
Keyword(s):  
Functional Diversity ◽  
Expression Patterns ◽  
Mads Box ◽  
Mads Box Genes

scholarly journals New Insights into the p38γ and p38δ MAPK Pathways

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Ana Risco ◽  
Ana Cuenda
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Protein Kinases ◽  
Expression Patterns ◽  
Cellular Functions ◽  
Mitogen Activated Protein Kinases ◽  
Pathological Conditions ◽  
Mitogen Activated Protein ◽  
Distinct Role ◽  
Made In

The mammalian p38 mitogen-activated protein kinases (MAPKs) family is composed of four members (p38α, p38β, p38γ, and p38δ), which are very similar in amino acid sequence but differ in their expression patterns. This suggests that they may have specific functions in different organs. In the last years most of the effort has been centred on the study of the function of the p38α isoform, which is widely referred to as p38 in the literature. However, the role that other p38 isoforms play in cellular functions and their implication in some of the pathological conditions have not been precisely defined so far. In this paper we highlight recent advances made in defining the functions of the two less studied alternative p38MAPKs, p38γ and p38δ. We describe that these p38MAPKs show similarities to the classical p38α isoform, although they may play central and distinct role in certain physiological and pathological processes.

scholarly journals EXPLICIT-Kinase: a gene expression predictor for dissecting the functions of the Arabidopsis kinome

2021 ◽  
Author(s):  
Yuming Peng ◽  
Wanzhu Zuo ◽  
Yue Qin ◽  
Shisong Ma
Keyword(s):  
Gene Expression ◽  
Protein Kinase ◽  
Protein Kinases ◽  
Stress Responses ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
The Novel ◽  
Cellular Processes ◽  
Bona Fide ◽  
Kinase A

Protein kinases regulate virtually all cellular processes, but it remains challenging to determine the functions of all protein kinases, collectively called the kinome, in any species. We developed an approach called EXPLICIT-Kinase to predict the functions of the Arabidopsis kinome. Because the activities of many kinases can be regulated transcriptionally, their gene expression patterns provide clues to their functions. A universal gene expression predictor for Arabidopsis was constructed to predict the expression of 30,172 non-kinase genes based on the expression of 994 protein kinase genes. The model reconstituted highly accurate transcriptomes for diverse Arabidopsis samples. It identified the significant kinases as predictor kinases for predicting the expression of Arabidopsis genes and pathways. Strikingly, these predictor kinases were often known regulators of the related pathways, as exemplified by those involved in cytokinesis, tissue development, and stress responses. Comparative analyses have revealed that portions of these predictor kinases, including the novel ones, are shared and conserved between Arabidopsis and maize. The conservation between species provide additional evidence to support the novel predictor kinases as bona fide regulators of the pathways involved. Thus our approach enables the systematic dissection of the functions of the Arabidopsis kinome.

scholarly journals Structural and functional diversity in the activity and regulation of DAPK-related protein kinases

FEBS Journal ◽  
2013 ◽  
Vol 280 (21) ◽  
pp. 5533-5550 ◽  
Author(s):  
Koen Temmerman ◽  
Bertrand Simon ◽  
Matthias Wilmanns
Keyword(s):  
Protein Kinases ◽  
Functional Diversity ◽  
Related Protein
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